recipe bioconductor-squallms

Speedy quality assurance via lasso labeling for LC-MS data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/squallms.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-squallms/meta.yaml

squallms is a Bioconductor R package that implements a "semi-labeled" approach to untargeted mass spectrometry data. It pulls in raw data from mass-spec files to calculate several metrics that are then used to label MS features in bulk as high or low quality. These metrics of peak quality are then passed to a simple logistic model that produces a fully-labeled dataset suitable for downstream analysis.

package bioconductor-squallms

versions:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-squallms

and update with::

   mamba update bioconductor-squallms

To create a new environment, run:

mamba create --name myenvname bioconductor-squallms

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-squallms:<tag>

(see `bioconductor-squallms/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-squallms/README.html)